Question: Gene profiling (RNA-seq or Microarray data) to explore public database to find similar samples
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gravatar for zhenyisong
3.4 years ago by
zhenyisong130
China
zhenyisong130 wrote:

My aim is to use the gene profiling of my sample (RNA-seq or Microarray data) to explore the database to find the similar samples. I used my sample and public data and performed Spearman correlation, but the result has a huge batch effect.Is there any implemented solution to my problems? Thanks.

ADD COMMENTlink modified 3.4 years ago by WouterDeCoster42k • written 3.4 years ago by zhenyisong130
1

Do you have problem with blasting huge number of transcriptome for annotation purposes or it is a batch effect problem ?

ADD REPLYlink written 3.4 years ago by Farbod3.3k

Hi zhenyisong,

Your title suggests you want to perform a blast search with many sequences (high-throughtput), however in your question you are using a correlation with gene expression profiling data... And you talk about batch effects...

I am a bit confused of what you are trying to do, and what you would like to hear from other Biostars users. Can you please explain better what you want to do and why? Maybe we can help.

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by Benn7.9k

@b.nota and @Farbod

Query input: a list of genes with their expression value. (my study result from microarray or RNA-seq data)

Database: archive all high-throughput results (microarray or RNA-seq) from various experiments

Output:

find the similar experiment in the database. I mean, I want to find the experiment deposited in my database which has a similar expression profile with my input.

I do not mean to use the BLAST engine to do the search task. I just mean if there is some implemented search strategy to find the most-like sample (experiment) with the provided gene profiling data. I hope I clarify my problem. Thanks.

ADD REPLYlink written 3.4 years ago by zhenyisong130
1

I edited your title to better reflect your question.

ADD REPLYlink written 3.4 years ago by WouterDeCoster42k

Thanks. It is just what I mean.

ADD REPLYlink written 3.4 years ago by zhenyisong130
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